I'd go through the wiring harness first, to see if any obvious breaks or shorts, anything loose enough so pushing or pulling triggers something.

LTG : )

Check your switches in switch test and make sure all are working correctly. Also check setting A2-47 and make sure the mini-playfield is not disabled.

Yep. Very good advice.

Would it still go up and down at all if it were disabled?

Another thing to check if switch test doesn't give you any useful information....

There are seven different connections (Wiring harnesses) for the MPF. As anyone who's had to take it out for adjusting is too familiar with lol. Run them all through a multimeter....you can test the ones cabinet-side by having the MPF out and then running through the tests for it seperately. You'll get a ton of errors because it thinks it's moving it up and down when it isn't, but what you want to check is that each thing is putting out (or cutting off) the same amount each time it runs through that test.

Be careful where you put fingers and metal things when you have it plugged in.

Normally the MPF does not work when it is disabled OR when your machine encounters an error in one of the optical switches (behind the white buttons). Mine had the same problem and I found out two of the optical switches where always triggered. It turned out that the receptors did not work on two buttons. I fixed it and the MPF worked like a charm (for two weeks, then a ball got stuck when the MPF was lowering and now it only rises an inch...)

I had some simular problems to this and it turned out to be a bad opto board. The time expander would never lock two balls as it was suposed to and at times it would cycle up / down on its own. The problem turned out to be a bad opto board even though the opto switch test were unremarkable. I replaced it with a board from GLM http://www.greatlakesmodular.com/ and all was well.